Paket: freecontact (1.0.21-13)

[ Quellcode: freecontact  ]

fast protein contact predictor

FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains the command line tool freecontact(1).

Andere Pakete mit Bezug zu freecontact

• dep: libboost-program-options1.74.0 (>= 1.74.0+ds1)

  C++-Bibliothek für Programmoptionen

• dep: libc6 (>= 2.34)

  GNU-C-Bibliothek: Laufzeitbibliotheken
  auch ein virtuelles Paket, bereitgestellt durch libc6-udeb

• dep: libfreecontact0v5 (>= 1.0.21)

  fast protein contact predictor library

• dep: libgcc-s1 (>= 3.0) [nicht armel, armhf]

  GCC Support-Bibliothek

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libstdc++6 (>= 11)

  GNU-Implementierung der Standard-C++-Bibliothek (Version 3)

• dep: libxerces-c3.2

  validating XML parser library for C++

• dep: perl

  Larry Wall's Practical Extraction und Report Language

• sug: bash-completion

  Programmierbare Vervollständigung für die Bash-Shell

• sug: hhsuite

  Sensible Proteinsequenzsuchen, basierend auf HMM-HMM-Alignment

• sug: hmmer

  Profil-Hidden-Markov-Modelle für Protein-Sequenzanalyse

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